no code implementations • 2 May 2021 • Adnan Akbar, Andrey Solovyev, John W Cassidy, Nirmesh Patel, Harry W Clifford
Identifying the mutations that drive cancer growth is key in clinical decision making and precision oncology.
no code implementations • 6 Dec 2019 • Geoffroy Dubourg-Felonneau, Omar Darwish, Christopher Parsons, Dami Rebergen, John W Cassidy, Nirmesh Patel, Harry W Clifford
Although these methods provide greater accuracy, classic neural networks lack the ability to indicate the confidence of a variant call.
no code implementations • 4 Dec 2019 • Geoffroy Dubourg-Felonneau, Omar Darwish, Christopher Parsons, Dami Rebergen, John W Cassidy, Nirmesh Patel, Harry W Clifford
The genomic profile underlying an individual tumor can be highly informative in the creation of a personalized cancer treatment strategy for a given patient; a practice known as precision oncology.
no code implementations • 28 Nov 2019 • Adnan Akbar, Geoffroy Dubourg-Felonneau, Andrey Solovyev, John W Cassidy, Nirmesh Patel, Harry W Clifford
Our proposed method is based on the intuition that if we can capture the true characteristics of sub-clones within a tumor and represent it in the form of features, a sophisticated machine learning algorithm can be trained to predict its behavior.
no code implementations • 27 Nov 2019 • Geoffroy Dubourg-Felonneau, Yasmeen Kussad, Dominic Kirkham, John W Cassidy, Nirmesh Patel, Harry W Clifford
In this study, we present Flatsomatic - a Variational Auto Encoder (VAE) optimized to compress somatic mutations that allow for unbiased data compression whilst maintaining the signal.
no code implementations • 20 Nov 2019 • Geoffroy Dubourg-Felonneau, Yasmeen Kussad, Dominic Kirkham, John W Cassidy, Nirmesh Patel, Harry W Clifford
Thus, the creation of low dimensional representations of somatic mutation profiles that hold useful information about the DNA of cancer cells will facilitate the use of such data in applications that will progress precision medicine.
no code implementations • 26 Nov 2018 • Luke R Harries, Suyi Zhang, Geoffroy Dubourg-Felonneau, James H R Farmery, Jonathan Sinai, Belle Taylor, Nirmesh Patel, John W Cassidy, John Shawe-Taylor, Harry W Clifford
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings.
no code implementations • 26 Nov 2018 • Geoffroy Dubourg-Felonneau, Timothy Cannings, Fergal Cotter, Hannah Thompson, Nirmesh Patel, John W Cassidy, Harry W Clifford
The potential benefits of applying machine learning methods to -omics data are becoming increasingly apparent, especially in clinical settings.